Just don't use brasso on them (Yes I remember you).
For CLEANING CD games, I normally clean them while they're under water, a little bit of soap on my hands. I've never had issues with them that way, since all the game CDs have printed labels on part of the CD. Old first gen CDs like for the TG-16 it might promote CD rot if you have a bad scratch, but I would think if it's that bad it'll still get CD rot no matter what. In your case it very well could have been the dust that scratched them, especially if you did it dry.
A real CD scratch removal system (NOT DISC DOCTOR!) would also be a good investment, they're $120-$160 for low end ones.